Metacat: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362012-06-05T18:48:34ZEcoinformatics Redmine
Redmine Bug #5616 (Resolved): See bug #5615 for EMLhttps://projects.ecoinformatics.org/ecoinfo/issues/56162012-06-05T18:48:34ZMargaret O'Brienmob@msi.ucsb.edu
<p>For good Metacat public relations, it is essential that EML documents be well- and completely presented.</p>
<p>The EML default HTML-skins need to be examined and then enhanced to make sure that they reflect good EML practice, and that labels and layout are intuitive to non-developers.</p>
<p>I made this a blocking issue, because to not do so before release would tarnish the reputation of Metacat. Others might disagree.</p> Bug #4676 (New): registry did not let me see my data table, although permissions are sethttps://projects.ecoinformatics.org/ecoinfo/issues/46762010-01-15T19:07:59ZMargaret O'Brienmob@msi.ucsb.edu
<p>I was demonstrating the knb dataset registry, and put in a test dataset (knb.230).<br />We logged in (as uid=mobrien,o=LTER...) While viewing the dataset, we clicked on the "View data table" link, and got the "public is not allowed to view this data table". I was still logged in, and the metadata for the data entity displayed an "authentication" value.</p> Bug #4658 (Resolved): metacat runs out of memoryhttps://projects.ecoinformatics.org/ecoinfo/issues/46582010-01-09T00:13:12ZMargaret O'Brienmob@msi.ucsb.edu
<p>I parsed an EML 201 doc from:<br /><a class="external" href="http://knb.ecoinformatics.org/emlparser/parse">http://knb.ecoinformatics.org/emlparser/parse</a></p>
<p>I got a java error to the effect that it ran out of memory trying to read a zip(?) I dont have the error trace any more.</p> Bug #4437 (New): allow-public-read rule is not being honoredhttps://projects.ecoinformatics.org/ecoinfo/issues/44372009-10-06T21:00:39ZMargaret O'Brienmob@msi.ucsb.edu
<p>This EML201 doc: knb-lter-sbc.3.7 contains 4 datatables. It has a dataset level access tree which includes an allow-public-read statment. Each data table also has additionalMetadata tree referencing it, also with allow-public-read statements. But one of the tables returns this message:</p>
<p>User public does not have permission to read the document with the docid sbclter.728.1</p>
<p>When you look at the doc, be sure to include the revision number. the most recent revision will have all those additionalMetadata trees removed.</p> Bug #4269 (Closed): EML from data.piscoweb not replicating to knbhttps://projects.ecoinformatics.org/ecoinfo/issues/42692009-07-27T19:49:02ZMargaret O'Brienmob@msi.ucsb.edu
<p>These 2 docs:<br /><a class="external" href="http://sbc.lternet.edu/catalog/metacat?action=read&qformat=sbclter&docid=SBCLTER_cruise-towed_TEMPLATE.1">http://sbc.lternet.edu/catalog/metacat?action=read&qformat=sbclter&docid=SBCLTER_cruise-towed_TEMPLATE.1</a><br /><a class="external" href="http://sbc.lternet.edu/catalog/metacat?action=read&qformat=sbclter&docid=SBCLTER_cruise-underway_TEMPLATE.1">http://sbc.lternet.edu/catalog/metacat?action=read&qformat=sbclter&docid=SBCLTER_cruise-underway_TEMPLATE.1</a></p>
<p>have not replicated to<br /><a class="external" href="http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=sbclter&docid=SBCLTER_cruise-towed_TEMPLATE.1">http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=sbclter&docid=SBCLTER_cruise-towed_TEMPLATE.1</a><br /><a class="external" href="http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=sbclter&docid=SBCLTER_cruise-underway_TEMPLATE.1">http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=sbclter&docid=SBCLTER_cruise-underway_TEMPLATE.1</a></p>
<p>They are both EML 2.0.1, and were inserted at data.piscoweb.org/.../dev/loadxml.html sometime in the last 2 weeks</p> Bug #4266 (Closed): error reading EML replicated to knbhttps://projects.ecoinformatics.org/ecoinfo/issues/42662009-07-27T18:20:32ZMargaret O'Brienmob@msi.ucsb.edu
<p>Replication of this dataset seems to have resulted in an error. It was inserted using the dev/loadxml.html page at metacat.lternet.edu on friday 7/24. On monday (7/27), this url correctly returned the document:<br />ttp://metacat.lternet.edu/knb/metacat?action=read&qformat=xml&docid=knb-lter-mcr.8.6</p>
<p>but this one:<br /><a class="external" href="http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=knb&docid=knb-lter-mcr.8.6">http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=knb&docid=knb-lter-mcr.8.6</a><br />returned <br /><error><br />Error reading document: knb-lter-mcr.8<br /></error><br />With the revision number (6) left off, the knb returns rev .5</p> Bug #4043 (Closed): lack of eml-access tree prohibits the doc owner from viewinghttps://projects.ecoinformatics.org/ecoinfo/issues/40432009-04-30T18:47:48ZMargaret O'Brienmob@msi.ucsb.edu
<p>This might be a question, rather than a bug.<br />This document was added to metacat v1.9.0 (at lter): sbc_eml210_test.1.1</p>
<p>It is a citation doc with no access tree. It was put in (and I assume owned by) either user=sbc or user=mobrien. Sorry, I can't tell you which user uploaded it.</p>
<p>I logged in as the user who is also the owner and tried to view the document (I tried this as both sbc and mobrien). I get the message that "user public does not have permission to view this doc"</p>
<p>Is this behavior planned? I know that the lack of an <access> tree means that the doc is not publicly accessible, but it seems like metacat should let the owner view the document after logging in.</p>
<p>Since the doc is small, I am including it here:<br /><?xml version="1.0" encoding="UTF-8"?><br /><eml:eml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" <br /> xmlns:eml="eml://ecoinformatics.org/eml-2.1.0" <br /> xsi:schemaLocation="eml://ecoinformatics.org/eml-2.1.0 eml.xsd" <br /> packageId="sbc_eml210_test.1.1" <br /> system="knb" <br /> scope="system"><br /> <citation id="sbc_eml210_test.1"><br /> <alternateIdentifier system="sbclter-bibliography">1</alternateIdentifier><br /> <title>The use of diatoms as indicators for water quality in streams and wetlands</title><br /> <creator scope="document"><br /> <individualName><br /> <givenName>L</givenName><br /> <surName>Busse</surName><br /> </individualName><br /> </creator><br /> <pubDate>2000</pubDate><br /> <presentation><br /> <conferenceName>Water Quality Meeting</conferenceName><br /> <conferenceLocation><br /> <deliveryPoint>University of California</deliveryPoint><br /> <city>Santa Barbara</city><br /> <administrativeArea>CA</administrativeArea><br /> </conferenceLocation><br /> </presentation><br /> </citation><br /></eml:eml></p> Bug #3889 (Resolved): KNB and LTER metacats not replicating some 210 test docshttps://projects.ecoinformatics.org/ecoinfo/issues/38892009-03-16T20:38:03ZMargaret O'Brienmob@msi.ucsb.edu
<p>Mike asked me to put this info into a bug.</p>
<p>sbc_eml210_test.6.2 (<a class="external" href="http://knb.ecoinformatics.org/knb/metacat/sbc_eml210_test.6.2/default">http://knb.ecoinformatics.org/knb/metacat/sbc_eml210_test.6.2/default</a><br />This doc was inserted directly to knb with the form at dev/style/skins/loadxml.html It does not appear at LTER.</p>
<p>5 other docs were inserted at LTER via dev/style/skins/loadxml.html but are not present at KNB<br />sbc_eml210_test.1.1 <a class="external" href="http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.1.1/lter">http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.1.1/lter</a><br />sbc_eml210_test.2.1 <a class="external" href="http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.2.1/lter">http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.2.1/lter</a><br />sbc_eml210_test.3.1 <a class="external" href="http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.3.1/lter">http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.3.1/lter</a><br />sbc_eml210_test.4.1 <a class="external" href="http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.4.1/lter">http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.4.1/lter</a><br />sbc_eml210_test.5.2 <a class="external" href="http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.5.2/lter">http://metacat.lternet.edu:8080/knb/metacat/sbc_eml210_test.5.2/lter</a></p>
<p>. <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: need more extensive element documentation (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1">#1</a> and <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: attribute editing for EMPTY elements doesn't work (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/2">#2</a> are citations, <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: some required elements should be optional (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/3#note-5">#3-5</a> are datasets. sbc_eml210_test.6.2 (at KNB) is identical to sbc_eml210_test.5.2 (at LNO), except for the docid, so there should be 6 documents total in both metacats.</p> Bug #2873 (Resolved): tomcat versions and java standard tag library (jstl)https://projects.ecoinformatics.org/ecoinfo/issues/28732007-06-14T17:37:56ZMargaret O'Brienmob@msi.ucsb.edu
<p>SBCLTER has a jsp application which uses jstl. The version of jstl needed depends on the tomcat and servlet versions. This is from <a class="external" href="http://jakarta.apache.org/taglibs/doc/standard-doc/intro.html">http://jakarta.apache.org/taglibs/doc/standard-doc/intro.html</a>:</p>
<p>Standard-1.1 (JSTL 1.1) requires a JSP container that supports the Java Servlet 2.4 and JavaServer Pages 2.0 specifications. Jakarta Tomcat 5 supports the new specifications. The Standard-1.1 taglib has been tested with Tomcat 5.0.3.<br />Standard-1.0 (implementation of the JSTL 1.0 specification) requires a JSP container that supports the Java Servlet 2.3 and JavaServer Pages 1.2 specifications. Jakarta Tomcat 4 supports these specifications. The Standard 1.0 taglib has been tested with Tomcat 4.1.24.</p>
<p>There are actually 2 jars: jstl.1.x.x.jar and standard.1.x.x.jar. Metacat 1.7 comes with the 1.0 libraries, and so I've had to switch to the 1.1 version. Also, the 1.0 and 1.1 jars can't both be included by default - only the correct one. (You probably already knew that, but it took me a day of head-scratching to get it).</p>
<p>The app that uses these libraries is at:<br />sbc.lternet.edu/publications</p>
<p>thanks!</p> Bug #2237 (Resolved): web.xml, tomcat and jstlhttps://projects.ecoinformatics.org/ecoinfo/issues/22372005-10-27T21:28:58ZMargaret O'Brienmob@msi.ucsb.edu
<p>I've been using JSP and Java Standard Tag Library functions with files in<br />metacat, and got tomcat5 errors because tomcat5 wants the web.xml file to be<br />pointing to this schema instead of the dtd used by tomcat3 and tomcat4:<br /> xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee<br /><a class="external" href="http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd">http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd</a>"</p>
<p>The tomcat errors occurred when using the jstl with the earlier dtd, but I had<br />no problems after switching to the schema in sbc's installation. Here is a<br />reference:<br /><a class="external" href="http://www.javaworld.com/javaforums/printthread.php?Cat=&Board=Enterprisejava&main=18070&type=thread">http://www.javaworld.com/javaforums/printthread.php?Cat=&Board=Enterprisejava&main=18070&type=thread</a></p>
<p>Two additional jar files are required to run jstl (jstl.jar, standard.jar). It<br />would be very convenient to see these included with metacat, although they are<br />also easily added by a user.</p> Bug #2236 (Resolved): metacat parser allows eml with missing contenthttps://projects.ecoinformatics.org/ecoinfo/issues/22362005-10-27T21:13:12ZMargaret O'Brienmob@msi.ucsb.edu
<p>Incomplete packages are allowed by the EML parser in metacat and at knb<br />(<a class="external" href="http://knb.ecoinformatics.org/emlparser/index.html">http://knb.ecoinformatics.org/emlparser/index.html</a>)<br />packages missing these nodes are allowed:<br />methods/methodStep/description/<br />methods/methodStep/protocol/creator/individualName/surName <br />An example in metacat is knb-lter-sbc.13.3. Morpho1.6rc1 chokes on these files,<br />so I checked the schema, and found that morpho was right. The example file was<br />most likely created with morpho1.4. Personally, I'd prefer you didnt fix this,<br />since it will make some of our existing packages invalid.</p>